We recommend using the manual dosing recommendations for all non-SWG pools including those using automation such as peristaltic pumps and The Liquidator. The minimum FC for manual dosing doesn't have much play in it -- if algae nutrients are high, you will be on the edge if you get even somewhat below the minimum. So the more continual automated dosing isn't the main reason the SWG numbers are lower. It might be a factor, but not the only one. The superchlorination in the SWG cell, which is high chlorine at low pH at the chlorine generation plate unlike dosing with hypochlorite which is high chlorine with high pH, is likely a factor (ultimately the SWG puts out the same chlorine and pH as hypochlorite after the high pH water from the hydrogen gas plate mixes with the low pH high chlorine water). The other factor is the higher salt level, though that is probably a smaller factor.
We simply don't know the real reason, but I'm guessing it's a little bit of all three in the order of most important to least of superchlorination, salt level and more continuous dosing.
If you wanted to operate at a lower FC/CYA level, you can use products to supplement slowing the growth of algae, but these are extra cost and some have side effects.